When Mobius Connect gets a $0 invoice from Manage, Manage also sends the tax code as tax exempt. We don't have an accurate way of determining what the tax code from Manage would have been if the invoice wasn't $0 so it stays at tax exempt.
To work around this, you have the following options:
1. Set a tax code for tax-exempt
2. Don't send $0 invoices to your accounting system. You can remove them from the Accounting Interface screen in Manage, and they'll stop showing up as unbatched within Mobius Connect.